From Point Groups to Space Groups

How to expand from a point group to a space groupSpecial and General Positions.Complete Hermann-Maugin Notation

Start with PtCl4

2-

D4h Character Table

Add Unique Symmetry

The Features

The view is looking down the 4-fold axis The square in the mirror represents the 4-fold

axis The bracket in the lower right corner is the

horizontal mirror The dashed lines are out of plane mirror planes Anything that can be placed on this template

has at least D4h symmetry

Comments on D4h

There are 16 symmetry operations The two-fold rotations perpendicular to the 4-

fold are generated by the mirrors. The 4-fold and the horizontal mirror are unique The H-M name is 4/mmm

Getting Rid of PtCl4

Question

Is it possible to place water into the D4h pattern?

Water has C2v symmetry which is very much lower than D4h so at first the answer would appear to be NO.

4 Waters in 4/mmm

In this packing the 2 of the water aligns with the 2 ofthe 4/mmm and the two mirrors align with thehorizontal and vertical mirrors! When the space groupand molecule share one or more symmetry elementsthe molecule is sitting on a special position!

8 Waters in 4/mmm

In this case only one of the mirrors on the water aligns with the horizontal mirror.The 2-fold and other mirror are not duplicated by the crystal symmetry.In this case the two hydrogen atoms are not symmetry relatedThe water can be rotated by 90º in which case there would only be one uniquehydrogen atomThe molecule still resides on a special position

In General

It is possible to place items with any or no symmetry in 4/mmm.

Place 8 above and 8 below the horizontal mirror plane.

Therefore there are 16 objects in the pattern Note D4h has 16 symmetry operations When an object is placed so no elements of the

space group pass through it it is said to be located on a general position.

The Crystallographic Symmetry

The crystallographic symmetry of fragment( that is a molecule, ion, etc.) is the symmetry of the site it occupies.

A fragment located on a general position has no symmetry in the crystal even if it appears to be quite symmetric.

A fragment on a special position has whatever the symmetry of the position is.

Fragment vs Crystal Symmetry

There is no correlation between the symmetry of a molecule and the cell it crystallizes in.

Very symmetric molecules crystallize in low symmetry cells.

Very asymmetric molecules can crystallize in surprisingly high symmetry cells

An Example

Crystallizes in a tetragonal space group!

Some Definitions

Asymmetric Unit – A unique part of the unit cell. When the symmetry operations are applied to the asymmetric unit the entire unit cell is created. The volume of the asymmetric unit is the volume of the unit cell divided by the number of symmetry operations (NSO)

Z—the number of formula units in the unit cell. Z'—the number of formula units in the

asymmetric unit = Z/NSO

Z must be an integer Z' can range from fractional to values > 1 Whenever Z' is non-integral it means that a

fragment is located on a special position. Whenever Z' is greater than 1 it means there is

more than one independent fragment in the asymmetric unit.

Lets look at this.

The International Tables for Crystallography can be found on-line as follows (note this only works from Purdue computers as the library pays for on-line access) Log on to http://www.iucr.org/ At the right click on the International Tables Click on Volume A which deals with symmetry Go to space group P4/mmm (no. 123)

Note space groups are like German Symphonies –they have a name and number/

Crystallographic Coordinates

The coordinates used to define the unit cell will always have the symmetry of the cell.

This requires that under any symmetry operation in the cell the axes go into themselves, - themselves or an equivalent axes.

This is not true for Cartesian coordinates where there is a 3-fold or 6-fold rotation axis.

For a 3-fold Axes

For this to work there must be 3 equivalent axes perpendicular to the 3-fold rotation.

Obviously it does not take 4 axes to define 3 dimensional space so one must be defined by the other two.

This is where the 4 indices hkil come from where i=-(h+k)

Hexangonal Axes

Note a3=-(a1+a2)

HomeworkLook at the Space Group P21/c (#14). This is

the most common space group for small molecules.

1. No protein has ever been found to crystallize in this space group. Why is that?

2. Someone reports a crystal in P21/c with Z=1.

Is this possible? Why or why not.

3. What is the symmetry of the special positions in this space group?